Balancing selection drives maintenance of genetic variation in Drosophila antimicrobial peptides

Genes involved in immune defense against pathogens provide some of the most well-known examples of both directional and balancing selection. Antimicrobial peptides (AMPs) are innate immune effector genes, playing a key role in pathogen clearance in many species, including Drosophila. Conflicting lines of evidence have suggested AMPs may be under directional, balancing or purifying selection. Here, we use a case-control gene approach to show that balancing selection is an important force shaping AMP diversity in two species of Drosophila. In D. melanogaster, this is most clearly observed in ancestral African populations. Furthermore, the signature of balancing selection is even clearer once background selection has been accounted for. Balancing selection also acts on AMPs in D. mauritiana, an isolated island endemic separated from D. melanogaster by about 4 million years of evolution. This suggests that balancing selection may be acting to maintain adaptive diversity in AMPs in insects, as it does in other taxa.